hp_ancestors {PCAN} | R Documentation

## HP ancestors (Example data)

### Description

HP terms which are ancestors of each HP term (including itself) in the Human Phenotype Ontology (http://www.human-phenotype-ontology.org/). Only descendants of 'Phenotypic abnormality' were taken into account.

### Format

A named list of 10962 character vectors.

### Details

These data are used to examplify the different functions of the package. More data are available in the MultiHumanPhenoDB package.

### Source

http://compbio.charite.de/hudson/job/hpo/1529/artifact/hp/hp.obo

### Examples

    ## Prerequisite
    data(geneByHp, hp_descendants, package="PCAN")
    geneByHp <- unstack(geneByHp, entrez~hp)
    ic <- computeHpIC(geneByHp, hp_descendants)

    ## Compute similarity between different couples of HP terms
    data(hp_ancestors, hpDef, package="PCAN")
    hp1 <- "HP:0000518"
    hp2 <- "HP:0030084"
    hp3 <- "HP:0002119"
    hp4 <- "HP:0001305"
    hpDef[which(hpDef$id %in% c(hp1, hp2)), 1:2]
    calcHpSim(hp1, hp2, IC=ic, ancestors=hp_ancestors)
    hpDef[which(hpDef$id %in% c(hp2, hp3)), 1:2]
    calcHpSim(hp2, hp3, IC=ic, ancestors=hp_ancestors)
    hpDef[which(hpDef$id %in% c(hp2, hp4)), 1:2]
    calcHpSim(hp2, hp4, IC=ic, ancestors=hp_ancestors)
    hpDef[which(hpDef$id %in% c(hp3, hp4)), 1:2]
    calcHpSim(hp3, hp4, IC=ic, ancestors=hp_ancestors)

[Package PCAN version 1.22.0 Index]